Starting phenix.real_space_refine
on Wed Mar 12 02:31:17 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8gcn_29936/03_2025/8gcn_29936.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gcn_29936/03_2025/8gcn_29936.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gcn_29936/03_2025/8gcn_29936.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gcn_29936/03_2025/8gcn_29936.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gcn_29936/03_2025/8gcn_29936.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gcn_29936/03_2025/8gcn_29936.cif"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4507      2.51       5
     N    1224      2.21       5
     O    1393      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7173
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 876, 6805
          Classifications: {'peptide': 876}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 37, 'TRANS': 838}
    Chain: "B"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 368
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
  Time building chain proxies: 4.12, per 1000 atoms: 0.57
  Number of scatterers: 7173
  At special positions: 0
  Unit cell: (81.096, 91.56, 112.488, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1393      8.00
     N    1224      7.00
     C    4507      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 914.6 milliseconds
  

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1760

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 0 sheets defined
      85.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 14 through 32
    Processing helix  chain 'A' and resid 32 through 46
      removed outlier: 3.524A  pdb=" N   ASN A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 66
    Processing helix  chain 'A' and resid 69 through 82
      removed outlier: 3.662A  pdb=" N   ALA A  82 " --> pdb=" O   GLN A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 99
      removed outlier: 3.646A  pdb=" N   LEU A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 124
      removed outlier: 4.250A  pdb=" N   GLN A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   CYS A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ALA A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 128 through 139
    Processing helix  chain 'A' and resid 143 through 161
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 169 through 181
      removed outlier: 4.007A  pdb=" N   ILE A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 202
      removed outlier: 3.788A  pdb=" N   LYS A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 210
      removed outlier: 3.894A  pdb=" N   ASP A 210 " --> pdb=" O   LYS A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 226
    Processing helix  chain 'A' and resid 230 through 248
    Processing helix  chain 'A' and resid 251 through 255
    Processing helix  chain 'A' and resid 259 through 270
    Processing helix  chain 'A' and resid 272 through 304
    Processing helix  chain 'A' and resid 313 through 330
      removed outlier: 5.536A  pdb=" N   GLN A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   TYR A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      Proline residue:  A 324  - end of helix
    Processing helix  chain 'A' and resid 343 through 360
    Processing helix  chain 'A' and resid 363 through 375
      Proline residue:  A 369  - end of helix
    Processing helix  chain 'A' and resid 379 through 393
      removed outlier: 3.690A  pdb=" N   ARG A 383 " --> pdb=" O   ASP A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 418
      removed outlier: 3.582A  pdb=" N   LEU A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      Proline residue:  A 404  - end of helix
      Proline residue:  A 411  - end of helix
      removed outlier: 3.987A  pdb=" N   LYS A 418 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 439
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 4.068A  pdb=" N   ALA A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 460
      removed outlier: 4.210A  pdb=" N   ALA A 450 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 463 through 486
      removed outlier: 4.676A  pdb=" N   ASN A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 501
    Processing helix  chain 'A' and resid 502 through 515
      removed outlier: 3.900A  pdb=" N   GLN A 508 " --> pdb=" O   GLU A 504 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS A 509 " --> pdb=" O   LEU A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 523
      removed outlier: 4.483A  pdb=" N   HIS A 520 " --> pdb=" O   PRO A 517 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   ASN A 522 " --> pdb=" O   GLY A 519 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN A 523 " --> pdb=" O   HIS A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 538
      removed outlier: 3.871A  pdb=" N   TYR A 529 " --> pdb=" O   ARG A 525 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLU A 530 " --> pdb=" O   SER A 526 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A 534 " --> pdb=" O   GLU A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 542
      No H-bonds generated for 'chain 'A' and resid 540 through 542'
    Processing helix  chain 'A' and resid 543 through 562
      removed outlier: 3.744A  pdb=" N   MET A 555 " --> pdb=" O   THR A 551 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   GLU A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG A 557 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 593
      removed outlier: 3.865A  pdb=" N   GLN A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG A 593 " --> pdb=" O   GLN A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 618
      removed outlier: 3.972A  pdb=" N   GLN A 602 " --> pdb=" O   GLN A 598 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ILE A 603 " --> pdb=" O   ASP A 599 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ASP A 605 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   VAL A 606 " --> pdb=" O   GLN A 602 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A 615 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   GLN A 616 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   THR A 618 " --> pdb=" O   MET A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 640
      removed outlier: 4.129A  pdb=" N   GLN A 625 " --> pdb=" O   SER A 621 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASP A 627 " --> pdb=" O   GLY A 623 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU A 629 " --> pdb=" O   GLN A 625 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   MET A 630 " --> pdb=" O   GLU A 626 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 635 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 649
      removed outlier: 4.753A  pdb=" N   LEU A 644 " --> pdb=" O   GLY A 641 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   LYS A 645 " --> pdb=" O   GLU A 642 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   MET A 647 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   GLU A 648 " --> pdb=" O   LYS A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 659
    Processing helix  chain 'A' and resid 663 through 682
      removed outlier: 3.984A  pdb=" N   CYS A 667 " --> pdb=" O   GLU A 663 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ARG A 679 " --> pdb=" O   GLY A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 702
      removed outlier: 4.063A  pdb=" N   ASP A 690 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   GLU A 691 " --> pdb=" O   PRO A 687 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 692 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 698 " --> pdb=" O   GLN A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 725
      removed outlier: 3.566A  pdb=" N   LEU A 714 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A 718 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ASP A 719 " --> pdb=" O   SER A 715 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 721 " --> pdb=" O   PHE A 717 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 722 " --> pdb=" O   GLY A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 745
      removed outlier: 4.371A  pdb=" N   GLU A 733 " --> pdb=" O   LYS A 729 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   VAL A 734 " --> pdb=" O   LYS A 730 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL A 735 " --> pdb=" O   TYR A 731 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 736 " --> pdb=" O   LEU A 732 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ASN A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A 741 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A 742 " --> pdb=" O   THR A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 778
    Processing helix  chain 'A' and resid 784 through 792
      removed outlier: 3.937A  pdb=" N   LEU A 789 " --> pdb=" O   ASP A 786 " (cutoff:3.500A)
      Proline residue:  A 792  - end of helix
    Processing helix  chain 'A' and resid 793 through 807
    Processing helix  chain 'A' and resid 811 through 829
      removed outlier: 3.546A  pdb=" N   GLY A 820 " --> pdb=" O   ALA A 816 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU A 821 " --> pdb=" O   CYS A 817 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ILE A 822 " --> pdb=" O   ALA A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 839
      removed outlier: 4.021A  pdb=" N   LYS A 835 " --> pdb=" O   LYS A 831 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LEU A 836 " --> pdb=" O   ASP A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 853
      removed outlier: 4.046A  pdb=" N   GLU A 845 " --> pdb=" O   PRO A 841 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR A 848 " --> pdb=" O   HIS A 844 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLU A 849 " --> pdb=" O   GLU A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 874
      removed outlier: 3.650A  pdb=" N   GLU A 868 " --> pdb=" O   TRP A 864 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS A 871 " --> pdb=" O   LYS A 867 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 17
    Processing helix  chain 'B' and resid 23 through 52

    497 hydrogen bonds defined for protein.
    1443 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 1.96 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1858
        1.33 -     1.45: 1169
        1.45 -     1.57: 4183
        1.57 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 7285
  Sorted by residual:
  bond pdb=" N   GLU A 493 "
       pdb=" CA  GLU A 493 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.04e-02 9.25e+03 7.99e+00
  bond pdb=" N   GLU A 492 "
       pdb=" CA  GLU A 492 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.15e+00
  bond pdb=" N   GLN A 491 "
       pdb=" CA  GLN A 491 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.17e-02 7.31e+03 5.97e+00
  bond pdb=" C   PRO A 494 "
       pdb=" O   PRO A 494 "
    ideal  model  delta    sigma   weight residual
    1.233  1.212  0.021 1.10e-02 8.26e+03 3.58e+00
  bond pdb=" CA  GLN A 491 "
       pdb=" C   GLN A 491 "
    ideal  model  delta    sigma   weight residual
    1.519  1.536 -0.016 1.01e-02 9.80e+03 2.60e+00
  ... (remaining 7280 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 9757
        2.91 -     5.82: 86
        5.82 -     8.74: 22
        8.74 -    11.65: 8
       11.65 -    14.56: 2
  Bond angle restraints: 9875
  Sorted by residual:
  angle pdb=" CA  LEU A 198 "
        pdb=" CB  LEU A 198 "
        pdb=" CG  LEU A 198 "
      ideal   model   delta    sigma   weight residual
     116.30  130.86  -14.56 3.50e+00 8.16e-02 1.73e+01
  angle pdb=" CA  LEU A 416 "
        pdb=" CB  LEU A 416 "
        pdb=" CG  LEU A 416 "
      ideal   model   delta    sigma   weight residual
     116.30  130.51  -14.21 3.50e+00 8.16e-02 1.65e+01
  angle pdb=" CB  LYS B  18 "
        pdb=" CG  LYS B  18 "
        pdb=" CD  LYS B  18 "
      ideal   model   delta    sigma   weight residual
     111.30  120.14   -8.84 2.30e+00 1.89e-01 1.48e+01
  angle pdb=" CB  MET A 555 "
        pdb=" CG  MET A 555 "
        pdb=" SD  MET A 555 "
      ideal   model   delta    sigma   weight residual
     112.70  123.54  -10.84 3.00e+00 1.11e-01 1.31e+01
  angle pdb=" CB  MET B  47 "
        pdb=" CG  MET B  47 "
        pdb=" SD  MET B  47 "
      ideal   model   delta    sigma   weight residual
     112.70  123.40  -10.70 3.00e+00 1.11e-01 1.27e+01
  ... (remaining 9870 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.01: 3786
       18.01 -    36.01: 533
       36.01 -    54.02: 139
       54.02 -    72.03: 31
       72.03 -    90.03: 21
  Dihedral angle restraints: 4510
    sinusoidal: 1810
      harmonic: 2700
  Sorted by residual:
  dihedral pdb=" CA  LEU A 562 "
           pdb=" C   LEU A 562 "
           pdb=" N   GLN A 563 "
           pdb=" CA  GLN A 563 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.64  -24.36     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  GLN A 563 "
           pdb=" C   GLN A 563 "
           pdb=" N   MET A 564 "
           pdb=" CA  MET A 564 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.57   22.43     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  ALA A 259 "
           pdb=" C   ALA A 259 "
           pdb=" N   LEU A 260 "
           pdb=" CA  LEU A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.44  -18.56     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1000
       0.059 -    0.118: 143
       0.118 -    0.177: 4
       0.177 -    0.236: 0
       0.236 -    0.295: 1
  Chirality restraints: 1148
  Sorted by residual:
  chirality pdb=" CG  LEU A 202 "
            pdb=" CB  LEU A 202 "
            pdb=" CD1 LEU A 202 "
            pdb=" CD2 LEU A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.88    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CB  THR A 863 "
            pdb=" CA  THR A 863 "
            pdb=" OG1 THR A 863 "
            pdb=" CG2 THR A 863 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CA  GLU A 493 "
            pdb=" N   GLU A 493 "
            pdb=" C   GLU A 493 "
            pdb=" CB  GLU A 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 1145 not shown)

  Planarity restraints: 1291
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 396 "   -0.043 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO A 397 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 397 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 397 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 490 "    0.013 2.00e-02 2.50e+03   2.58e-02 6.65e+00
        pdb=" C   ASP A 490 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 490 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A 491 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 479 "   -0.010 2.00e-02 2.50e+03   2.07e-02 4.29e+00
        pdb=" CD  GLU A 479 "    0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 479 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 479 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1288 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 169
        2.67 -     3.23: 8007
        3.23 -     3.79: 12435
        3.79 -     4.34: 15526
        4.34 -     4.90: 23268
  Nonbonded interactions: 59405
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 547 "
            pdb=" OG1 THR A 551 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OG1 THR A 827 "
            pdb=" OE2 GLU A 868 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OD1 ASP A 690 "
            pdb=" OH  TYR A 731 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" O   LEU A 847 "
            pdb=" NH1 ARG A 851 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OE2 GLU A 398 "
            pdb=" OG  SER A 400 "
     model   vdw
     2.204 3.040
  ... (remaining 59400 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.820
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7285  Z= 0.213
  Angle     :  0.777  14.562   9875  Z= 0.369
  Chirality :  0.041   0.295   1148
  Planarity :  0.004   0.065   1291
  Dihedral  : 18.905  90.034   2750
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 33.42 %
    Favored  : 66.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.29), residues: 915
  helix:  0.66 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.49 (0.46), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  80 
 HIS   0.002   0.001   HIS A 706 
 PHE   0.014   0.001   PHE A 577 
 TYR   0.031   0.001   TYR A 482 
 ARG   0.005   0.000   ARG B  39 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 MET cc_start: 0.9580 (mmm) cc_final: 0.9291 (mmm)
REVERT: B   20 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8237 (mmmm)
REVERT: B   30 ARG cc_start: 0.9475 (mtp85) cc_final: 0.8980 (mtp85)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1819
  time to fit residues: 19.4744
Evaluate side-chains
  72 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    2.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 522 ASN
A 569 GLN
A 576 GLN
A 660 ASN
A 684 ASN
A 712 GLN
A 737 ASN
A 759 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.054961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.040122 restraints weight = 50733.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.041468 restraints weight = 32880.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.042446 restraints weight = 24418.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7285  Z= 0.226
  Angle     :  0.677  10.358   9875  Z= 0.338
  Chirality :  0.040   0.132   1148
  Planarity :  0.004   0.064   1291
  Dihedral  :  4.205  21.869    982
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 27.22 %
    Favored  : 69.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.29), residues: 915
  helix:  0.66 (0.20), residues: 710
  sheet:  None (None), residues: 0
  loop : -0.40 (0.49), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 472 
 HIS   0.002   0.001   HIS A 706 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.016   0.001   TYR A 482 
 ARG   0.003   0.001   ARG B  39 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: A  472 TRP cc_start: 0.9294 (OUTLIER) cc_final: 0.8659 (m-90)
REVERT: A  482 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8993 (m-80)
REVERT: B   30 ARG cc_start: 0.9499 (mtp85) cc_final: 0.9071 (mtp85)
  outliers start: 24
  outliers final: 12
  residues processed: 100
  average time/residue: 0.1691
  time to fit residues: 23.8635
Evaluate side-chains
  90 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  458 GLU
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 88 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 78 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 3 optimal weight:   20.0000
   overall best weight:    5.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 521 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.053552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.038901 restraints weight = 52747.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.040189 restraints weight = 33957.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.041135 restraints weight = 25191.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7285  Z= 0.306
  Angle     :  0.706   9.229   9875  Z= 0.358
  Chirality :  0.042   0.149   1148
  Planarity :  0.004   0.065   1291
  Dihedral  :  4.308  23.095    982
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 19.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 27.09 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.28), residues: 915
  helix:  0.57 (0.19), residues: 716
  sheet:  None (None), residues: 0
  loop : -0.43 (0.49), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 472 
 HIS   0.005   0.001   HIS A 706 
 PHE   0.016   0.002   PHE A 577 
 TYR   0.021   0.002   TYR A 482 
 ARG   0.004   0.001   ARG A 613 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 78
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9050 (mm) cc_final: 0.8759 (mm)
REVERT: A  472 TRP cc_start: 0.9336 (OUTLIER) cc_final: 0.8654 (m-90)
REVERT: A  482 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.8955 (m-80)
REVERT: A  551 THR cc_start: 0.9643 (m) cc_final: 0.9425 (p)
REVERT: A  589 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8564 (pp30)
REVERT: A  608 MET cc_start: 0.9056 (tmm) cc_final: 0.8811 (ppp)
REVERT: B   30 ARG cc_start: 0.9470 (mtp85) cc_final: 0.8874 (mtp85)
  outliers start: 38
  outliers final: 20
  residues processed: 104
  average time/residue: 0.1808
  time to fit residues: 26.1340
Evaluate side-chains
  98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  730 LYS
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 70 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:   30.0000
   chunk 82 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0870
   chunk 81 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    3.6166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 741 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.054180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.039377 restraints weight = 52831.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.040721 restraints weight = 33566.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.041697 restraints weight = 24764.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7285  Z= 0.241
  Angle     :  0.702  10.425   9875  Z= 0.348
  Chirality :  0.042   0.268   1148
  Planarity :  0.004   0.062   1291
  Dihedral  :  4.241  22.433    982
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 16.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 28.61 %
    Favored  : 67.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.28), residues: 915
  helix:  0.69 (0.19), residues: 716
  sheet:  None (None), residues: 0
  loop : -0.45 (0.49), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 472 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.016   0.001   PHE A 577 
 TYR   0.021   0.001   TYR A 482 
 ARG   0.004   0.000   ARG B  39 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9011 (mm) cc_final: 0.8710 (mm)
REVERT: A  198 LEU cc_start: 0.9499 (tt) cc_final: 0.9244 (pp)
REVERT: A  252 MET cc_start: 0.9596 (mmm) cc_final: 0.9301 (mmp)
REVERT: A  472 TRP cc_start: 0.9294 (OUTLIER) cc_final: 0.8641 (m-90)
REVERT: A  482 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8993 (m-80)
REVERT: A  588 LEU cc_start: 0.9434 (mm) cc_final: 0.9227 (mm)
REVERT: A  589 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8497 (pp30)
REVERT: A  608 MET cc_start: 0.9088 (tmm) cc_final: 0.8840 (ppp)
REVERT: A  614 MET cc_start: 0.9294 (ppp) cc_final: 0.9032 (ppp)
REVERT: B   30 ARG cc_start: 0.9496 (mtp85) cc_final: 0.9053 (mtp85)
  outliers start: 32
  outliers final: 21
  residues processed: 99
  average time/residue: 0.1776
  time to fit residues: 24.6509
Evaluate side-chains
  99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 69 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:   40.0000
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.054271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.039707 restraints weight = 51578.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.041125 restraints weight = 32456.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.042124 restraints weight = 23571.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7285  Z= 0.219
  Angle     :  0.688  10.221   9875  Z= 0.340
  Chirality :  0.041   0.204   1148
  Planarity :  0.004   0.062   1291
  Dihedral  :  4.161  21.554    982
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 28.35 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.28), residues: 915
  helix:  0.84 (0.20), residues: 711
  sheet:  None (None), residues: 0
  loop : -0.44 (0.48), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 472 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.016   0.001   PHE A 577 
 TYR   0.021   0.001   TYR A 482 
 ARG   0.005   0.000   ARG B  39 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.8979 (mm) cc_final: 0.8674 (mm)
REVERT: A  198 LEU cc_start: 0.9503 (tt) cc_final: 0.9249 (pp)
REVERT: A  290 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9117 (mm-30)
REVERT: A  472 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.8611 (m-90)
REVERT: A  482 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8963 (m-80)
REVERT: A  588 LEU cc_start: 0.9429 (mm) cc_final: 0.9125 (mm)
REVERT: A  614 MET cc_start: 0.9256 (ppp) cc_final: 0.9029 (ppp)
REVERT: B   30 ARG cc_start: 0.9502 (mtp85) cc_final: 0.9071 (mtp85)
  outliers start: 32
  outliers final: 22
  residues processed: 100
  average time/residue: 0.1789
  time to fit residues: 25.1077
Evaluate side-chains
  99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 74 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.053940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.039663 restraints weight = 50713.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.041048 restraints weight = 31960.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.042012 restraints weight = 23362.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7285  Z= 0.237
  Angle     :  0.726  12.593   9875  Z= 0.355
  Chirality :  0.042   0.187   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.116  19.578    982
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 28.10 %
    Favored  : 67.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.28), residues: 915
  helix:  0.90 (0.20), residues: 711
  sheet:  None (None), residues: 0
  loop : -0.40 (0.47), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  80 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.021   0.001   TYR A 482 
 ARG   0.004   0.000   ARG B  31 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 75
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9004 (mm) cc_final: 0.8703 (mm)
REVERT: A  198 LEU cc_start: 0.9485 (tt) cc_final: 0.9237 (pp)
REVERT: A  472 TRP cc_start: 0.9281 (OUTLIER) cc_final: 0.8611 (m-90)
REVERT: A  482 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8937 (m-80)
REVERT: A  533 MET cc_start: 0.9172 (mmt) cc_final: 0.8825 (mmt)
REVERT: B   30 ARG cc_start: 0.9479 (mtp85) cc_final: 0.9053 (mtp85)
  outliers start: 38
  outliers final: 26
  residues processed: 101
  average time/residue: 0.1819
  time to fit residues: 25.6321
Evaluate side-chains
  101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 86 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 14 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.053731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.039374 restraints weight = 51363.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.040760 restraints weight = 32218.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.041696 restraints weight = 23439.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7285  Z= 0.252
  Angle     :  0.738  13.628   9875  Z= 0.363
  Chirality :  0.043   0.275   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.227  20.801    982
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 29.49 %
    Favored  : 66.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.28), residues: 915
  helix:  0.86 (0.20), residues: 719
  sheet:  None (None), residues: 0
  loop : -0.39 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  80 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.021   0.001   TYR A 482 
 ARG   0.008   0.001   ARG B  29 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9070 (mm) cc_final: 0.8772 (mm)
REVERT: A  198 LEU cc_start: 0.9470 (tt) cc_final: 0.9254 (pp)
REVERT: A  252 MET cc_start: 0.9446 (mmm) cc_final: 0.9241 (mmp)
REVERT: A  290 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.9130 (mm-30)
REVERT: A  472 TRP cc_start: 0.9305 (OUTLIER) cc_final: 0.8735 (m-90)
REVERT: A  482 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.8227 (m-80)
REVERT: B   30 ARG cc_start: 0.9482 (mtp85) cc_final: 0.9037 (mtp85)
  outliers start: 31
  outliers final: 27
  residues processed: 99
  average time/residue: 0.1790
  time to fit residues: 24.7950
Evaluate side-chains
  101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 71
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.053979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.039612 restraints weight = 51688.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.041008 restraints weight = 32444.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.042007 restraints weight = 23613.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7285  Z= 0.230
  Angle     :  0.743  13.542   9875  Z= 0.365
  Chirality :  0.043   0.270   1148
  Planarity :  0.004   0.060   1291
  Dihedral  :  4.170  20.485    982
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 30.00 %
    Favored  : 65.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 915
  helix:  0.87 (0.19), residues: 719
  sheet:  None (None), residues: 0
  loop : -0.41 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  80 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.014   0.001   PHE A 577 
 TYR   0.019   0.001   TYR A 482 
 ARG   0.005   0.000   ARG B  29 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 76
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9037 (mm) cc_final: 0.8734 (mm)
REVERT: A  198 LEU cc_start: 0.9467 (tt) cc_final: 0.9244 (pp)
REVERT: A  252 MET cc_start: 0.9450 (mmm) cc_final: 0.9224 (mmp)
REVERT: A  290 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9144 (mm-30)
REVERT: A  472 TRP cc_start: 0.9322 (OUTLIER) cc_final: 0.8862 (m-90)
REVERT: A  533 MET cc_start: 0.9176 (mmt) cc_final: 0.8832 (mmt)
REVERT: B   30 ARG cc_start: 0.9474 (mtp85) cc_final: 0.9051 (mtp85)
  outliers start: 35
  outliers final: 26
  residues processed: 97
  average time/residue: 0.1784
  time to fit residues: 24.1718
Evaluate side-chains
  102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  146 MET
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 0 optimal weight:   40.0000
   chunk 88 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9990
   chunk 74 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 81 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.054486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.039816 restraints weight = 51839.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.041246 restraints weight = 32582.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.042253 restraints weight = 23663.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7285  Z= 0.209
  Angle     :  0.755  13.446   9875  Z= 0.369
  Chirality :  0.043   0.266   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.149  21.455    982
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 30.38 %
    Favored  : 65.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.28), residues: 915
  helix:  0.88 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -0.52 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  80 
 HIS   0.002   0.000   HIS A 706 
 PHE   0.014   0.001   PHE A 577 
 TYR   0.015   0.001   TYR A 482 
 ARG   0.006   0.000   ARG B  29 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9034 (mm) cc_final: 0.8727 (mm)
REVERT: A  198 LEU cc_start: 0.9440 (tt) cc_final: 0.9206 (pp)
REVERT: A  252 MET cc_start: 0.9474 (mmm) cc_final: 0.9237 (mmp)
REVERT: A  290 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9145 (mm-30)
REVERT: A  472 TRP cc_start: 0.9295 (OUTLIER) cc_final: 0.8848 (m-90)
REVERT: A  482 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8723 (m-80)
REVERT: A  533 MET cc_start: 0.9167 (mmt) cc_final: 0.8939 (mmt)
REVERT: B   30 ARG cc_start: 0.9466 (mtp85) cc_final: 0.9070 (mtp85)
  outliers start: 33
  outliers final: 27
  residues processed: 101
  average time/residue: 0.1797
  time to fit residues: 25.4191
Evaluate side-chains
  107 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  146 MET
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 46 optimal weight:    0.5980
   chunk 75 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    3.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.053952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.039479 restraints weight = 51968.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.040884 restraints weight = 32501.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.041857 restraints weight = 23593.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7285  Z= 0.252
  Angle     :  0.786  14.746   9875  Z= 0.387
  Chirality :  0.043   0.253   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.206  20.529    982
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 31.52 %
    Favored  : 64.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.28), residues: 915
  helix:  0.85 (0.20), residues: 716
  sheet:  None (None), residues: 0
  loop : -0.39 (0.48), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  80 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.014   0.001   PHE A 577 
 TYR   0.009   0.001   TYR A 382 
 ARG   0.005   0.000   ARG B  29 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 75
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9009 (mm) cc_final: 0.8708 (mm)
REVERT: A  252 MET cc_start: 0.9465 (mmm) cc_final: 0.9213 (mmp)
REVERT: A  472 TRP cc_start: 0.9315 (OUTLIER) cc_final: 0.8921 (m-90)
REVERT: A  482 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8780 (m-10)
REVERT: A  533 MET cc_start: 0.9178 (mmt) cc_final: 0.8852 (mmt)
REVERT: A  859 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9355 (mtmm)
REVERT: B   20 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8306 (mtmm)
REVERT: B   30 ARG cc_start: 0.9468 (mtp85) cc_final: 0.9065 (mtp85)
  outliers start: 32
  outliers final: 26
  residues processed: 96
  average time/residue: 0.2001
  time to fit residues: 26.5969
Evaluate side-chains
  104 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  146 MET
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain A residue  859 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 56 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 83 optimal weight:    0.1980
   chunk 74 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 72 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    4.4388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.053351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.038793 restraints weight = 53614.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.040168 restraints weight = 33261.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.041158 restraints weight = 24199.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7285  Z= 0.284
  Angle     :  0.804  14.531   9875  Z= 0.394
  Chirality :  0.044   0.335   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.286  20.962    982
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 18.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 31.39 %
    Favored  : 64.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.28), residues: 915
  helix:  0.77 (0.19), residues: 715
  sheet:  None (None), residues: 0
  loop : -0.36 (0.49), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  80 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.015   0.002   PHE A 577 
 TYR   0.010   0.001   TYR A 382 
 ARG   0.005   0.000   ARG B  29 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2365.71 seconds
wall clock time: 41 minutes 51.97 seconds (2511.97 seconds total)